Ciobanu Doina, Clum Alicia, Ahrendt Steven, Andreopoulos William B, Salamov Asaf, Chan Sandy, Quandt C Alisha, Foster Brian, Meier-Kolthoff Jan P, Tang Yung Tsu, Schwientek Patrick, Benny Gerald L, Smith Matthew E, Bauer Diane, Deshpande Shweta, Barry Kerrie, Copeland Alex, Singer Steven W, Woyke Tanja, Grigoriev Igor V, James Timothy Y, Cheng Jan-Fang
US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA.
iScience. 2021 Mar 10;24(4):102290. doi: 10.1016/j.isci.2021.102290. eCollection 2021 Apr 23.
Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes.
环境微生物的单细胞测序是微生物生态学工具包的重要组成部分。然而，针对未培养真核生物进行全基因组恢复的大规模靶向单细胞测序仍较为滞后。关键挑战在于环境群落中的低丰度、庞大复杂的基因组以及难以打破的细胞壁。我们描述了一种流程，该流程由最先进的单细胞基因组学工具和协议组成，这些工具和协议针对在低丰度下发现的研究较少且未培养的真核微生物进行了优化。此流程包括七个不同步骤，从样本采集开始，到基因组注释结束，每个步骤都配备了质量审查步骤，以确保以低成本获得高质量的基因组。我们在真菌以及色藻/不等鞭毛类早期分化谱系的环境样本和培养物上对每个步骤进行了测试和评估。我们表明，使用该流程产生的基因组对于环境微生物真核生物的功能和比较基因组学而言，几乎与完整的参考基因组一样出色。
Zotero 插件
